I've got a few updates to put on but I haven't found a good/easy way to compress the photos so that they can be uploaded to this site.
I managed to get the boot floor to meet up to the rear arch much better than in the last pics. Clamping the floor to the rear quarter took up most of the gap. I think it also took a bit of hammering and reshaping of the bottom of the rear arch to close the gap up a bit. The inside rear corner of the arch where it meets the boot floor was also holding the floor off and had to be reshaped slightly. Once I got it close enough, I then put a seam weld across the rear bottom edge of the arch and the boot floor and plug welded the rear quarter lip to the boot floor.
The better way to close the gap with the rear valance and the closing plate would be to fabricate a small piece to take it up to the edge of the valance. I on the other hand, filled it with weld and then ground it back, rather effective I thought but using a piece of sheet metal would have been soo much easier.